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- PDB-7yfv: Structure of Rpgrip1l CC1 -

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Basic information

Entry
Database: PDB / ID: 7yfv
TitleStructure of Rpgrip1l CC1
ComponentsProtein fantom
KeywordsPROTEIN BINDING / STRUCTURAL PROTEIN
Function / homology
Function and homology information


thromboxane A2 receptor binding / nose development / neural tube patterning / lateral ventricle development / establishment of planar polarity / head development / ciliary transition zone / photoreceptor connecting cilium / pericardium development / axonemal microtubule ...thromboxane A2 receptor binding / nose development / neural tube patterning / lateral ventricle development / establishment of planar polarity / head development / ciliary transition zone / photoreceptor connecting cilium / pericardium development / axonemal microtubule / Hedgehog 'off' state / limb morphogenesis / Anchoring of the basal body to the plasma membrane / telencephalon development / corpus callosum development / olfactory bulb development / non-motile cilium assembly / camera-type eye development / regulation of smoothened signaling pathway / embryonic forelimb morphogenesis / determination of left/right symmetry / embryonic hindlimb morphogenesis / negative regulation of G protein-coupled receptor signaling pathway / ciliary rootlet / cochlea development / establishment or maintenance of cell polarity / axoneme / cilium assembly / bicellular tight junction / cerebellum development / liver development / kidney development / brain development / cell-cell junction / in utero embryonic development / ciliary basal body / cilium / centrosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RPGR-interacting protein 1, first C2 domain / RPGRIP1 family / RPGRIP1, C-terminal / First C2 domain of RPGR-interacting protein 1 / Retinitis pigmentosa G-protein regulator interacting C-terminal / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å
AuthorsHe, R. / Chen, G. / Li, Z. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Iscience / Year: 2023
Title: Structure of the N-terminal coiled-coil domains of the ciliary protein Rpgrip1l.
Authors: He, R. / Chen, G. / Li, Z. / Li, J.
History
DepositionJul 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein fantom
B: Protein fantom
C: Protein fantom
D: Protein fantom


Theoretical massNumber of molelcules
Total (without water)28,5294
Polymers28,5294
Non-polymers00
Water73941
1
A: Protein fantom
B: Protein fantom


Theoretical massNumber of molelcules
Total (without water)14,2652
Polymers14,2652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area8100 Å2
MethodPISA
2
C: Protein fantom
D: Protein fantom


Theoretical massNumber of molelcules
Total (without water)14,2652
Polymers14,2652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-10 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.167, 104.674, 38.413
Angle α, β, γ (deg.)90.000, 105.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein fantom / Nephrocystin-8 / RPGR-interacting protein 1-like protein / RPGRIP1-like protein


Mass: 7132.267 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rpgrip1l, Ftm, Nphp8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CG73
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 7.5% w/v PEG6000, 0.1 M Sodium citrate tribasic dihydrate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13799 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Χ2: 0.476 / Net I/σ(I): 4.2 / Num. measured all: 94590
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.70.8076900.7860.3320.8740.42899.3
2.24-2.287.10.6276760.8680.250.6760.4599.6
2.28-2.3270.5416750.9060.2170.5830.43999.6
2.32-2.3770.57210.9080.2010.5390.44699.6
2.37-2.4270.4036520.9370.1620.4350.45199.1
2.42-2.4870.366890.9430.1460.3890.46799.4
2.48-2.5470.3257120.960.1310.350.46999.4
2.54-2.616.90.2636540.9730.1070.2840.47299.2
2.61-2.696.70.226890.9730.0910.2380.51499.4
2.69-2.776.30.1837090.9820.0780.1990.49999.7
2.77-2.876.70.1566700.9880.0650.1690.50499.9
2.87-2.997.20.1357080.9920.0540.1460.5299.9
2.99-3.127.20.1086650.9940.0430.1160.50499.7
3.12-3.297.10.0876990.9950.0350.0930.53599.7
3.29-3.4970.0737080.9970.0290.0790.54599.9
3.49-3.766.90.0636710.9970.0260.0680.56399.6
3.76-4.146.30.0516980.9980.0220.0550.525100
4.14-4.746.90.0426960.9990.0170.0460.463100
4.74-5.9770.0447100.9980.0180.0470.394100
5.97-506.40.037070.9990.0120.0330.32999

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→29.1 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 690 5.01 %
Rwork0.2138 13086 -
obs0.2163 13776 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.07 Å2 / Biso mean: 57.653 Å2 / Biso min: 30.57 Å2
Refinement stepCycle: final / Resolution: 2.2→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 0 41 1616
Biso mean---53.74 -
Num. residues----190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.350.29581440.2522253896
2.35-2.590.2841210.2363261499
2.59-2.960.24811290.2332665100
2.96-3.730.2811410.22062621100
3.73-29.10.24761550.19362648100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2046-4.56023.35445.7261-6.00485.0332-0.0792-0.21960.29790.03480.1661-0.2703-0.1376-0.158-0.1250.4219-0.051-0.04310.48960.03030.5023-4.99236.22915.43
28.6181-4.10376.76713.0597-3.82865.6554-1.08890.70560.9886-0.83960.7530.6528-0.6469-1.21850.29110.5704-0.092-0.07070.58310.10640.6924-5.18915.04227.69
3-0.1615-2.09211.29218.2803-7.05835.57320.02120.10280.1735-0.54490.0631-0.40120.2288-0.29140.10040.3390.01490.04130.360.070.48111.32135.6767.968
42.0867-0.4237-0.28534.11182.26131.33660.2679-2.2518-1.60761.4271-0.21380.08370.0637-0.05150.3080.8858-0.0293-0.15961.2718-0.06470.597321.23230.45430.813
51.99553.71473.80584.82825.08064.1864-0.45950.07820.214-0.55190.27370.2248-0.40660.50790.1350.3902-0.070.00360.437-0.06340.431912.59716.8825.728
63.8337-0.14191.80048.4163-1.15654.66260.8530.81090.25880.41360.32560.2563-0.5298-0.2028-1.09640.74650.0107-0.09450.5901-0.11021.094516.1740.47119.014
71.39931.32071.28085.43296.42738.4237-0.1066-0.18610.21550.66620.10370.26330.9650.35740.12830.39560.005-0.0210.47830.00830.324611.00112.40714.425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:46 )A3 - 46
2X-RAY DIFFRACTION2( CHAIN B AND RESID 0:5 )B0 - 5
3X-RAY DIFFRACTION3( CHAIN B AND RESID 6:48 )B6 - 48
4X-RAY DIFFRACTION4( CHAIN C AND RESID 1:5 )C1 - 5
5X-RAY DIFFRACTION5( CHAIN C AND RESID 6:47 )C6 - 47
6X-RAY DIFFRACTION6( CHAIN D AND RESID 1:5 )D1 - 5
7X-RAY DIFFRACTION7( CHAIN D AND RESID 6:46 )D6 - 46

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